Post process #138

ck768 · 2025-10-29T02:43:36Z

No description provided.

hhy2022 · 2026-01-14T18:02:01Z

book/content/post_process/exports.md

+]
+```
+
+These `.bp` exports can then be viewed in Paraview.


In the following subsection, you discuss ParaView in more detail. It might be helpful in this subsection to include a link or brief pointer indicating that the next section will cover how to use ParaView.

hhy2022 · 2026-01-14T18:05:03Z

book/content/post_process/multi_material_paraview.png

The figure would be clearer with units added to the color bar.

I don't agree, the point here is to show the "raw" visualisation inside paraview. As in what would the users see if they simply open this file in paraview.

In the Paraview section we can go in details and show how to customise the colourbar etc

hhy2022 · 2026-01-14T18:07:38Z

book/content/post_process/paraview/paraview_changing_variables.png

Could we display the figure with all selectable parameters shown in the drop-down menu?

hhy2022 · 2026-01-14T18:09:41Z

book/content/post_process/pyvista.md

+    figure = u_plotter.screenshot("concentration.png")
+```
+
+## Plotting the solution for continuous problems ##


This subtitle seems the same as the previous one?

Suggested change

## Plotting the solution for continuous problems ##

## Plotting the solution for discontinuous problems ##

RemDelaporteMathurin

@ck768 a few comments on my side

RemDelaporteMathurin · 2026-01-14T19:04:25Z

book/content/post_process/pyvista.md

+
+# Using PyVista for interactive visualization #
+
+PyVista has many helpful capabilities for 3D visualization based on VTK code, and is used frequently throughout the FESTIM workshop. Users can use PyVista in Jupyter Notebook to visualize fields and meshes interactively. 


We should state that this is not suitable for transient data. Throughout the workshop we use it to display either steady state data, or the final timestep.

RemDelaporteMathurin · 2026-01-14T19:04:50Z

book/content/post_process/pyvista.md

+pyvista.start_xvfb()
+pyvista.set_jupyter_backend("html")


Since this is only useful for the workshop on RTD, I would put it in a separate hidden cell

RemDelaporteMathurin · 2026-01-14T19:05:25Z

book/content/post_process/pyvista.md

+def make_ugrid(solution):
+    topology, cell_types, geometry = plot.vtk_mesh(solution.function_space)
+    u_grid = pyvista.UnstructuredGrid(topology, cell_types, geometry)
+    u_grid.point_data["c"] = solution.x.array.real
+    u_grid.set_active_scalars("c")
+    return u_grid


Having this function here may be confusing. This is a tutorial on pyvista so let's break things down step by step to make sure readers understand the building blocks

Especially since in this specific example you only use the function once

RemDelaporteMathurin · 2026-01-14T19:12:25Z

book/content/post_process/pyvista.md

+u_plotter = pyvista.Plotter()
+u_grid = make_ugrid(H.post_processing_solution)
+u_plotter.add_mesh(u_grid, cmap="viridis", show_edges=False)
+u_plotter.view_xy()
+u_plotter.add_text("Hydrogen concentration", font_size=12)
+
+if not pyvista.OFF_SCREEN:
+    u_plotter.show()
+else:
+    figure = u_plotter.screenshot("concentration.png")


Since this is the pyvista interactive viz tutorial, i think it is extremely important to break this down more granularly.

"First we instanciate a Plotter object, then we use the dolfinx function plot.vtk_mesh with the functionspace of itnerest, here the solution's functionspace to get the topology, the cell_types, the geometry, which are needed to make a pyvista UnstructuredGrid object. Then we attach point data to this grid, etc."

RemDelaporteMathurin · 2026-01-14T19:13:53Z

book/content/post_process/pyvista.md

+    figure = u_plotter.screenshot("concentration.png")
+```
+
+## Plotting the solution for continuous problems ##


Suggested change

## Plotting the solution for continuous problems ##

## Plotting the solution for discontinuous problems ##

RemDelaporteMathurin · 2026-01-14T19:57:36Z

book/content/post_process/paraview.md

+  name: python3
+---
+
+# Viewing exports in Paraview #


Suggested change

# Viewing exports in Paraview #

# Visualising fields in Paraview #

RemDelaporteMathurin · 2026-01-14T19:59:05Z

book/content/post_process/paraview.md

+
+++
+
+## Creating a VTX species export  ##


After this code cell we should say what the users should expect to see (ie. the creation of a folder called "paraview/out.bp")

RemDelaporteMathurin · 2026-01-14T19:59:20Z

book/content/post_process/paraview.md

+
+## Creating a VTX species export  ##
+
+First, let us run a simple 2D diffusion problem and export a VTK file:


Suggested change

First, let us run a simple 2D diffusion problem and export a VTK file:

First, let us run a simple 2D diffusion problem and export to VTX:

RemDelaporteMathurin · 2026-01-14T20:05:48Z

book/content/post_process/paraview.md

+  name: python3
+---
+
+# Viewing exports in Paraview #


I like the step-by-step guide. We should extend this with:

the special case of a 1D field where you need to Plot Over Line

some basic paraview features:

changing the colourbar

slicing (using 3D data)

plotting a profile

transient data and time controls (play, back, forward...)

RemDelaporteMathurin · 2026-01-14T20:06:45Z

book/content/post_process/paraview.md

+Then, we select our `out.bp` file and press OK on the bottom:
+
+```{image} paraview/paraview_selecting_file.png
+:class: bg-primary mb-1
+:align: center
+```
+


I think the first time you open a .bp file a pop up windows shows up and you need to select from 2 or 3 readers.

ckhurana and others added 11 commits October 22, 2025 11:34

adding post processing

50baa36

post process chapter, pyvista and paraview incomplete

1d7659d

adding post processing

5a40694

post process chapter, pyvista and paraview incomplete

a6ff5d8

pulled from festim2

27223b2

broken link

c09c9af

almost done, xdmf not writing correctly

876b1c8

added markdown files

9b9db83

changed jupyter version to < 2

145455b

fixed image names

71f58d5

added note with proper syntax

3b66c94

ck768 marked this pull request as ready for review January 9, 2026 15:19

hhy2022 reviewed Jan 14, 2026

View reviewed changes

RemDelaporteMathurin requested changes Jan 14, 2026

View reviewed changes

	## Plotting the solution for continuous problems ##
	## Plotting the solution for discontinuous problems ##


		# Using PyVista for interactive visualization #

		PyVista has many helpful capabilities for 3D visualization based on VTK code, and is used frequently throughout the FESTIM workshop. Users can use PyVista in Jupyter Notebook to visualize fields and meshes interactively.

	# Viewing exports in Paraview #
	# Visualising fields in Paraview #


		## Creating a VTX species export ##

		First, let us run a simple 2D diffusion problem and export a VTK file:

		pyvista.start_xvfb()
		pyvista.set_jupyter_backend("html")

Post process #138

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Post process #138

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ck768 commented Oct 29, 2025

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